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Stephen Harper’s claims that he was in the dark for months about the “criminal acts” run out of his office in the controversy over Sen. Mike Duffy’s expenses defy belief, opposition MPs charged Monday.

OTTAWA—Stephen Harper’s claims that he was in the dark for months about the “criminal acts” run out of his office in the controversy over Sen. Mike Duffy’s expenses defy belief, opposition MPs charged Monday.

Using the latest RCMP court filings as ammunition, NDP Leader Thomas Mulcair pressed the Conservatives on Harper’s apparent approval of a deal to pay Duffy’s disputed living expenses.

“Does the prime minister agree that there was a criminal cover-up organized out of his own office,” Mulcair said in question period.

Opposition MPs are on a renewed attack after an RCMP court filing last week provided new revelations into the controversy that saw Harper’s former chief of staff Nigel Wright cut a personal cheque to cover Duffy’s improperly claimed living expenses.

The most recent RCMP court filing says there are “reasonable grounds” to believe Duffy and Wright committed Criminal Code offences, namely bribery, fraud on the government and breach of trust, using their offices “for a dishonest purpose, other than for the public good.” None of the allegations has been proven in court.

At one point that day, Wright emails PMO lawyer Benjamin Perrin, “I do want to speak to the PM before everything is considered final.”

Less than an hour later Wright writes, “We are good to go from the PM.”

Harper’s officials now say that the prime minister was simply reiterating what he told Duffy personally on Feb. 13 — repay the living the expenses. Harper had said he was deceived by his own staff.

But Mulcair said Monday that version of events doesn’t make sense.

“Why would Nigel Wright have to get approval on Feb. 22 for something the prime minister claims he had already ordered nine days earlier,” the NDP leader said.

Harper was not in the Commons Monday, leaving his parliamentary secretary Paul Calandra to field the opposition questions.

Calandra said that even after Harper gave the order to repay his living expenses, Duffy continued to resist and argued that he was entitled to the claims.

“Sen. Duffy had no intention of repaying those inappropriate expenses,” Calandra said.

But opposition MPs were skeptical, saying it’s not reasonable to expect that Harper, known for keeping a tight rein over his government, was not aware of the scheme that unfolded over many weeks within his own office.

“If we are to believe him, then there was unethical and potentially illegal activity in his office. Not only was he kept in the dark, but his top aides actually lied to the prime minister,” said NDP MP Megan Leslie.

Calandra said that Harper was also unaware that influential Conservative Sen. Irving Gerstein had contacted Deloitte — at the insistence of the PMO — to influence the outcome of an ongoing independent audit of Duffy’s expenses, according to the RCMP documents.

Mulcair questioned why Wright had been punished for his role but Gerstein remains in the party, where he serves as head of the Conservative Fund.

“The prime minister says all of this was wrong and he would never have approved any of it. If that is true then why has the prime minister not removed Mr. Gerstein from the Conservative caucus,” he said in the Commons.

Meanwhile, the RCMP probe is broadening into the Senate as investigators seek emails sent or received by Duffy and former Conservative colleagues in the Senate: Marjory LeBreton, Carolyn Stewart Olsen, and David Tkachuk.

A review of emails from PMO email accounts has revealed that “all of these Senators have used their Senate email accounts to communicate about the matter of the Senate investigation into Senator Duffy’s expenses,” RCMP Cpl. Greg Horton said in his filing released last week.

He’s seeking the emails for the period Jan. 1 to May 19, 2013.

The RCMP indicate the scope of their investigation of the emails will be limited to Deloitte’s audit of Duffy’s expenses and the Senate’s Internal Economy investigation of and subsequent report on Duffy’s claims.

LeBreton told the Star that the question of whether the emails will be released is in the hands of Speaker Noël Kinsella.

“When I was interviewed I was fully expecting the RCMP to ask for my emails and was surprised that they did not,” LeBreton wrote in an email. “If they had done so, I would have fully co-operated. It will be up to the Speaker to make the decision from the Senate’s perspective.”

Senate communications refused to comment on Monday, as the matter is under police investigation. But in the Information To Obtain production order, the RCMP indicated that Senate Clerk Gary O’Brien has preserved the emails in question and that the data will be handed over.

Stewart Olsen also refused comment. In an interview last week after the ITO was released, Tkachuk said the RCMP had previously asked for his emails but he “wanted to think about it.” He later said he had no objection with releasing the emails.

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